Multiple sequence alignment - TraesCS5A01G428700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G428700 chr5A 100.000 3625 0 0 1 3625 613475388 613479012 0.000000e+00 6695.0
1 TraesCS5A01G428700 chr5A 91.589 107 7 2 3048 3154 435033260 435033364 2.920000e-31 147.0
2 TraesCS5A01G428700 chr5D 88.949 2398 115 68 709 3055 490996949 490999247 0.000000e+00 2822.0
3 TraesCS5A01G428700 chr5D 93.568 482 24 6 3148 3625 490999245 490999723 0.000000e+00 712.0
4 TraesCS5A01G428700 chr5D 89.669 484 45 4 1 481 490996291 490996772 2.390000e-171 612.0
5 TraesCS5A01G428700 chr5D 93.000 100 7 0 519 618 510940978 510941077 2.920000e-31 147.0
6 TraesCS5A01G428700 chr5D 79.433 141 17 6 2676 2805 9944034 9943895 4.990000e-14 89.8
7 TraesCS5A01G428700 chr5B 89.217 1456 77 29 621 2021 605784381 605785811 0.000000e+00 1746.0
8 TraesCS5A01G428700 chr5B 92.194 1012 50 13 2069 3055 605785813 605786820 0.000000e+00 1404.0
9 TraesCS5A01G428700 chr5B 89.095 486 20 14 3148 3621 605786818 605787282 1.130000e-159 573.0
10 TraesCS5A01G428700 chr5B 89.781 274 26 1 2 275 605783404 605783675 2.070000e-92 350.0
11 TraesCS5A01G428700 chr5B 93.204 103 7 0 3051 3153 425880118 425880220 6.270000e-33 152.0
12 TraesCS5A01G428700 chr5B 78.014 141 19 6 2676 2805 10099851 10099712 1.080000e-10 78.7
13 TraesCS5A01G428700 chr4D 93.458 107 5 2 3050 3154 93339457 93339351 1.350000e-34 158.0
14 TraesCS5A01G428700 chr4D 90.566 106 9 1 524 628 318607622 318607517 4.880000e-29 139.0
15 TraesCS5A01G428700 chr3B 91.964 112 8 1 3038 3149 110451958 110452068 4.850000e-34 156.0
16 TraesCS5A01G428700 chr3B 92.381 105 6 2 3049 3152 171174297 171174194 8.110000e-32 148.0
17 TraesCS5A01G428700 chr7D 93.137 102 7 0 3052 3153 474338721 474338822 2.250000e-32 150.0
18 TraesCS5A01G428700 chr7D 93.000 100 7 0 522 621 30953113 30953212 2.920000e-31 147.0
19 TraesCS5A01G428700 chr7D 83.088 136 11 3 2688 2811 34373465 34373330 2.960000e-21 113.0
20 TraesCS5A01G428700 chr7D 83.088 136 11 3 2688 2811 34756871 34757006 2.960000e-21 113.0
21 TraesCS5A01G428700 chr7B 91.667 108 8 1 519 625 217312363 217312256 8.110000e-32 148.0
22 TraesCS5A01G428700 chr7B 93.590 78 4 1 2687 2763 59069360 59069283 8.230000e-22 115.0
23 TraesCS5A01G428700 chr6D 92.381 105 6 2 517 621 389646673 389646571 8.110000e-32 148.0
24 TraesCS5A01G428700 chr6D 90.909 110 9 1 3053 3162 464266281 464266173 2.920000e-31 147.0
25 TraesCS5A01G428700 chr6D 82.895 152 11 8 2667 2805 147883721 147883870 4.920000e-24 122.0
26 TraesCS5A01G428700 chr4B 84.756 164 8 5 2681 2833 78607614 78607771 8.110000e-32 148.0
27 TraesCS5A01G428700 chr3D 91.667 108 5 4 3052 3158 177818769 177818873 2.920000e-31 147.0
28 TraesCS5A01G428700 chr2B 93.814 97 6 0 522 618 361570388 361570484 2.920000e-31 147.0
29 TraesCS5A01G428700 chr7A 90.090 111 9 2 3049 3159 645464550 645464658 3.770000e-30 143.0
30 TraesCS5A01G428700 chr7A 79.104 134 18 6 2677 2802 19262196 19262327 2.320000e-12 84.2
31 TraesCS5A01G428700 chr3A 91.262 103 9 0 522 624 648862932 648863034 1.360000e-29 141.0
32 TraesCS5A01G428700 chr1B 89.381 113 9 3 515 625 301472179 301472068 4.880000e-29 139.0
33 TraesCS5A01G428700 chr4A 89.815 108 10 1 522 629 679975760 679975866 1.760000e-28 137.0
34 TraesCS5A01G428700 chr4A 83.704 135 11 2 2688 2811 690411436 690411302 2.290000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G428700 chr5A 613475388 613479012 3624 False 6695.00 6695 100.000000 1 3625 1 chr5A.!!$F2 3624
1 TraesCS5A01G428700 chr5D 490996291 490999723 3432 False 1382.00 2822 90.728667 1 3625 3 chr5D.!!$F2 3624
2 TraesCS5A01G428700 chr5B 605783404 605787282 3878 False 1018.25 1746 90.071750 2 3621 4 chr5B.!!$F2 3619

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
242 245 0.962356 GGTCATCACCAGCCCAAGTG 60.962 60.0 0.0 0.0 43.17 3.16 F
1436 1905 0.450583 TCCTCTTGATTCGTCGTCCG 59.549 55.0 0.0 0.0 38.13 4.79 F
1487 1957 0.109039 GTCCTGCTCTGAAGACCGAC 60.109 60.0 0.0 0.0 0.00 4.79 F
2112 2630 0.523072 AATGCTGTCGAACATGGCAC 59.477 50.0 0.0 0.0 33.12 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1936 0.251386 TCGGTCTTCAGAGCAGGACT 60.251 55.000 6.81 0.00 42.28 3.85 R
2437 2955 0.608308 ACTAAACAAGGAAGCCGGCC 60.608 55.000 26.15 8.83 0.00 6.13 R
2438 2956 2.007608 CTACTAAACAAGGAAGCCGGC 58.992 52.381 21.89 21.89 0.00 6.13 R
2933 3468 2.158385 ACCCTGTGGTTAGCAAAATGGA 60.158 45.455 0.00 0.00 44.75 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 9.430399 AATGGAAGGAATCTCATCAATAATTGT 57.570 29.630 0.00 0.00 0.00 2.71
97 98 2.418334 GCCCTCGTAGAACCGATCTTTT 60.418 50.000 0.00 0.00 39.71 2.27
102 103 5.080969 TCGTAGAACCGATCTTTTGGATT 57.919 39.130 0.00 0.00 39.71 3.01
128 130 3.067833 GACTTCTTGTTAGTGCACCTCC 58.932 50.000 14.63 1.40 0.00 4.30
178 180 8.217799 TCTTTAGAACTGGAATCTTTCTTTGGA 58.782 33.333 0.00 0.00 31.93 3.53
179 181 8.760980 TTTAGAACTGGAATCTTTCTTTGGAA 57.239 30.769 0.00 0.00 31.93 3.53
180 182 6.890979 AGAACTGGAATCTTTCTTTGGAAG 57.109 37.500 0.00 0.00 32.61 3.46
185 188 5.860611 TGGAATCTTTCTTTGGAAGTACGA 58.139 37.500 0.00 0.00 32.61 3.43
222 225 1.196012 GAGTCTACACTTCCAGGGGG 58.804 60.000 0.00 0.00 30.63 5.40
242 245 0.962356 GGTCATCACCAGCCCAAGTG 60.962 60.000 0.00 0.00 43.17 3.16
285 645 2.315925 TCTCTTTAGATGGGCAAGCG 57.684 50.000 0.00 0.00 0.00 4.68
309 670 6.705381 CGAAGGAGCTCATTGAAATCTCTATT 59.295 38.462 19.88 0.00 0.00 1.73
311 672 7.134362 AGGAGCTCATTGAAATCTCTATTGA 57.866 36.000 17.19 0.00 0.00 2.57
327 688 7.212976 TCTCTATTGATAGTCAAGTTCATGCC 58.787 38.462 0.00 0.00 40.05 4.40
368 729 2.581354 GCTCCGGTCTGACTGCAT 59.419 61.111 11.18 0.00 0.00 3.96
382 743 7.201565 GGTCTGACTGCATTATCTTAGTTGAAC 60.202 40.741 7.85 0.00 0.00 3.18
389 750 5.450550 GCATTATCTTAGTTGAACCCTTGGC 60.451 44.000 0.00 0.00 0.00 4.52
391 752 3.586470 TCTTAGTTGAACCCTTGGCAA 57.414 42.857 0.00 0.00 0.00 4.52
428 789 6.428771 TCAAAAAGTTATTACCGTGGAGAAGG 59.571 38.462 0.00 0.00 0.00 3.46
484 847 6.844696 TTCAACAGCTACTTTGTCTACTTG 57.155 37.500 0.00 0.00 0.00 3.16
486 849 5.983720 TCAACAGCTACTTTGTCTACTTGTC 59.016 40.000 0.00 0.00 0.00 3.18
488 851 6.163135 ACAGCTACTTTGTCTACTTGTCTT 57.837 37.500 0.00 0.00 0.00 3.01
517 955 6.701432 AAAGACTTTTCCATTCGTAGTACG 57.299 37.500 16.65 16.65 44.19 3.67
518 956 5.382618 AGACTTTTCCATTCGTAGTACGT 57.617 39.130 21.38 1.09 43.14 3.57
519 957 6.500684 AGACTTTTCCATTCGTAGTACGTA 57.499 37.500 21.38 13.34 43.14 3.57
521 959 7.542025 AGACTTTTCCATTCGTAGTACGTATT 58.458 34.615 21.38 0.00 43.14 1.89
522 960 8.677300 AGACTTTTCCATTCGTAGTACGTATTA 58.323 33.333 21.38 6.35 43.14 0.98
523 961 8.620533 ACTTTTCCATTCGTAGTACGTATTAC 57.379 34.615 21.38 16.03 43.14 1.89
525 963 8.841444 TTTTCCATTCGTAGTACGTATTACTC 57.159 34.615 21.38 0.00 43.14 2.59
526 964 7.552458 TTCCATTCGTAGTACGTATTACTCA 57.448 36.000 21.38 11.13 43.14 3.41
528 966 6.763135 TCCATTCGTAGTACGTATTACTCACT 59.237 38.462 21.38 8.15 43.14 3.41
529 967 7.042456 TCCATTCGTAGTACGTATTACTCACTC 60.042 40.741 21.38 0.25 43.14 3.51
530 968 6.589830 TTCGTAGTACGTATTACTCACTCC 57.410 41.667 21.38 0.00 43.14 3.85
531 969 4.740205 TCGTAGTACGTATTACTCACTCCG 59.260 45.833 21.38 8.46 43.14 4.63
532 970 4.504461 CGTAGTACGTATTACTCACTCCGT 59.496 45.833 21.42 0.00 40.48 4.69
534 972 5.886960 AGTACGTATTACTCACTCCGTTT 57.113 39.130 0.00 0.00 36.09 3.60
535 973 5.873732 AGTACGTATTACTCACTCCGTTTC 58.126 41.667 0.00 0.00 36.09 2.78
537 975 5.125100 ACGTATTACTCACTCCGTTTCAA 57.875 39.130 0.00 0.00 0.00 2.69
538 976 5.531634 ACGTATTACTCACTCCGTTTCAAA 58.468 37.500 0.00 0.00 0.00 2.69
539 977 5.984926 ACGTATTACTCACTCCGTTTCAAAA 59.015 36.000 0.00 0.00 0.00 2.44
540 978 6.647895 ACGTATTACTCACTCCGTTTCAAAAT 59.352 34.615 0.00 0.00 0.00 1.82
542 980 8.318876 CGTATTACTCACTCCGTTTCAAAATAG 58.681 37.037 0.00 0.00 0.00 1.73
545 983 6.727824 ACTCACTCCGTTTCAAAATAGATG 57.272 37.500 0.00 0.00 0.00 2.90
547 985 6.369065 ACTCACTCCGTTTCAAAATAGATGAC 59.631 38.462 0.00 0.00 0.00 3.06
548 986 6.464222 TCACTCCGTTTCAAAATAGATGACT 58.536 36.000 0.00 0.00 0.00 3.41
549 987 6.590292 TCACTCCGTTTCAAAATAGATGACTC 59.410 38.462 0.00 0.00 0.00 3.36
550 988 5.577164 ACTCCGTTTCAAAATAGATGACTCG 59.423 40.000 0.00 0.00 0.00 4.18
551 989 5.716094 TCCGTTTCAAAATAGATGACTCGA 58.284 37.500 0.00 0.00 0.00 4.04
552 990 5.575606 TCCGTTTCAAAATAGATGACTCGAC 59.424 40.000 0.00 0.00 0.00 4.20
553 991 5.577164 CCGTTTCAAAATAGATGACTCGACT 59.423 40.000 0.00 0.00 0.00 4.18
554 992 6.090898 CCGTTTCAAAATAGATGACTCGACTT 59.909 38.462 0.00 0.00 0.00 3.01
555 993 7.360101 CCGTTTCAAAATAGATGACTCGACTTT 60.360 37.037 0.00 0.00 0.00 2.66
556 994 8.644619 CGTTTCAAAATAGATGACTCGACTTTA 58.355 33.333 0.00 0.00 0.00 1.85
608 1046 6.683974 AGTTGGGTCATCTATTTTGAATCG 57.316 37.500 0.00 0.00 0.00 3.34
609 1047 5.590259 AGTTGGGTCATCTATTTTGAATCGG 59.410 40.000 0.00 0.00 0.00 4.18
610 1048 5.366482 TGGGTCATCTATTTTGAATCGGA 57.634 39.130 0.00 0.00 0.00 4.55
611 1049 5.940617 TGGGTCATCTATTTTGAATCGGAT 58.059 37.500 0.00 0.00 0.00 4.18
612 1050 5.764686 TGGGTCATCTATTTTGAATCGGATG 59.235 40.000 0.00 0.00 33.92 3.51
613 1051 5.182001 GGGTCATCTATTTTGAATCGGATGG 59.818 44.000 0.00 0.00 33.59 3.51
614 1052 5.997746 GGTCATCTATTTTGAATCGGATGGA 59.002 40.000 0.00 0.00 33.59 3.41
619 1057 7.361457 TCTATTTTGAATCGGATGGAGTACT 57.639 36.000 0.00 0.00 0.00 2.73
637 1075 3.828875 ACTAGTTAGCTGCCCAATCTC 57.171 47.619 0.00 0.00 0.00 2.75
655 1093 1.391485 CTCGAGTCTCGCCATTGTTTG 59.609 52.381 17.61 0.00 40.21 2.93
656 1094 1.148310 CGAGTCTCGCCATTGTTTGT 58.852 50.000 9.74 0.00 31.14 2.83
657 1095 1.531149 CGAGTCTCGCCATTGTTTGTT 59.469 47.619 9.74 0.00 31.14 2.83
658 1096 2.032030 CGAGTCTCGCCATTGTTTGTTT 60.032 45.455 9.74 0.00 31.14 2.83
677 1115 1.719529 TGGAAGGTACGGTGGAAGAA 58.280 50.000 0.00 0.00 0.00 2.52
680 1118 3.839490 TGGAAGGTACGGTGGAAGAAATA 59.161 43.478 0.00 0.00 0.00 1.40
683 1121 5.296035 GGAAGGTACGGTGGAAGAAATAATG 59.704 44.000 0.00 0.00 0.00 1.90
696 1134 6.991531 GGAAGAAATAATGCCCAATAATTGCA 59.008 34.615 0.00 0.00 39.68 4.08
715 1153 1.004044 CAGGCAACAGGAAGAGGACAT 59.996 52.381 0.00 0.00 41.41 3.06
722 1160 4.686191 ACAGGAAGAGGACATGATGATC 57.314 45.455 0.00 0.00 0.00 2.92
759 1197 1.721389 CCGATCGCCAATAATCAGTCG 59.279 52.381 10.32 0.00 0.00 4.18
762 1200 3.361053 CGATCGCCAATAATCAGTCGTAC 59.639 47.826 0.26 0.00 0.00 3.67
763 1201 4.547532 GATCGCCAATAATCAGTCGTACT 58.452 43.478 0.00 0.00 0.00 2.73
776 1214 1.670811 GTCGTACTGCCAATTCCATGG 59.329 52.381 4.97 4.97 43.70 3.66
803 1241 1.804151 TGCAGGAAACGGAAAGAATCG 59.196 47.619 0.00 0.00 0.00 3.34
885 1334 1.228429 CCGCAAGTGAAAAGGGGGA 60.228 57.895 0.00 0.00 35.55 4.81
892 1341 2.436115 GAAAAGGGGGAGCGTCCG 60.436 66.667 0.00 0.00 37.43 4.79
1417 1886 3.892284 ACAGTATCTGACATCGTCCTCT 58.108 45.455 3.70 0.00 35.18 3.69
1418 1887 3.880490 ACAGTATCTGACATCGTCCTCTC 59.120 47.826 3.70 0.00 35.18 3.20
1419 1888 3.252215 CAGTATCTGACATCGTCCTCTCC 59.748 52.174 0.00 0.00 32.44 3.71
1420 1889 2.746279 ATCTGACATCGTCCTCTCCT 57.254 50.000 0.00 0.00 0.00 3.69
1421 1890 2.045561 TCTGACATCGTCCTCTCCTC 57.954 55.000 0.00 0.00 0.00 3.71
1432 1901 2.017782 TCCTCTCCTCTTGATTCGTCG 58.982 52.381 0.00 0.00 0.00 5.12
1433 1902 1.746220 CCTCTCCTCTTGATTCGTCGT 59.254 52.381 0.00 0.00 0.00 4.34
1435 1904 1.743958 TCTCCTCTTGATTCGTCGTCC 59.256 52.381 0.00 0.00 0.00 4.79
1436 1905 0.450583 TCCTCTTGATTCGTCGTCCG 59.549 55.000 0.00 0.00 38.13 4.79
1437 1906 1.140407 CCTCTTGATTCGTCGTCCGC 61.140 60.000 0.00 0.00 36.19 5.54
1438 1907 0.456142 CTCTTGATTCGTCGTCCGCA 60.456 55.000 0.00 0.00 36.19 5.69
1439 1908 0.456142 TCTTGATTCGTCGTCCGCAG 60.456 55.000 0.00 0.00 36.19 5.18
1440 1909 0.456142 CTTGATTCGTCGTCCGCAGA 60.456 55.000 0.00 0.00 36.19 4.26
1441 1910 0.456142 TTGATTCGTCGTCCGCAGAG 60.456 55.000 0.00 0.00 36.19 3.35
1455 1924 4.742649 AGAGAGGGAGTCGCGGCA 62.743 66.667 15.58 0.00 0.00 5.69
1467 1936 2.359850 GCGGCAGGGTGATGTGAA 60.360 61.111 0.00 0.00 0.00 3.18
1477 1946 1.277557 GGTGATGTGAAGTCCTGCTCT 59.722 52.381 0.00 0.00 0.00 4.09
1487 1957 0.109039 GTCCTGCTCTGAAGACCGAC 60.109 60.000 0.00 0.00 0.00 4.79
1541 2011 5.644188 ACTGATTTCATTCCCCTTTCTTCA 58.356 37.500 0.00 0.00 0.00 3.02
1543 2013 6.379417 ACTGATTTCATTCCCCTTTCTTCATC 59.621 38.462 0.00 0.00 0.00 2.92
1606 2091 4.787286 TGCAACATACGGGCGGGG 62.787 66.667 0.00 0.00 0.00 5.73
1621 2106 2.127232 GGGGCGAATGTTCCATGGG 61.127 63.158 13.02 0.00 0.00 4.00
1689 2181 4.932200 AGTGACTGAAATGAATCGGAAGTC 59.068 41.667 0.00 0.00 34.52 3.01
1725 2217 5.651139 GGGACTCACTCTGTAATACAGTACA 59.349 44.000 18.71 0.65 46.03 2.90
1726 2218 6.404513 GGGACTCACTCTGTAATACAGTACAC 60.405 46.154 18.71 6.69 46.03 2.90
1727 2219 6.374894 GGACTCACTCTGTAATACAGTACACT 59.625 42.308 18.71 0.68 46.03 3.55
1728 2220 7.551974 GGACTCACTCTGTAATACAGTACACTA 59.448 40.741 18.71 0.00 46.03 2.74
1729 2221 8.495361 ACTCACTCTGTAATACAGTACACTAG 57.505 38.462 18.71 10.76 46.03 2.57
1749 2241 8.082852 ACACTAGTAGTAATAATCATGCCTTCG 58.917 37.037 1.57 0.00 0.00 3.79
1794 2286 2.376808 AATCTTCAGCTCCTGTCGTG 57.623 50.000 0.00 0.00 32.61 4.35
1834 2332 3.395639 GTCACGAAACCCTGTTATGTCA 58.604 45.455 0.00 0.00 0.00 3.58
1839 2337 4.454504 ACGAAACCCTGTTATGTCATTCAC 59.545 41.667 0.00 0.00 0.00 3.18
1844 2342 3.696051 CCCTGTTATGTCATTCACTTGGG 59.304 47.826 0.00 2.24 0.00 4.12
1845 2343 4.335416 CCTGTTATGTCATTCACTTGGGT 58.665 43.478 0.00 0.00 0.00 4.51
1846 2344 4.156556 CCTGTTATGTCATTCACTTGGGTG 59.843 45.833 0.00 0.00 44.23 4.61
1856 2354 1.898574 ACTTGGGTGCGCTGAAAGG 60.899 57.895 9.73 0.00 0.00 3.11
1879 2377 3.654020 GCCGAGATGCCCGCATTC 61.654 66.667 3.24 3.28 36.70 2.67
1888 2386 2.435372 TGCCCGCATTCCTTTTAGAT 57.565 45.000 0.00 0.00 0.00 1.98
1897 2395 4.440663 GCATTCCTTTTAGATGAGTTGCCC 60.441 45.833 0.00 0.00 0.00 5.36
1929 2434 3.865745 AGGAAAGAATATCAGACGCAACG 59.134 43.478 0.00 0.00 0.00 4.10
1953 2464 3.264193 TCACCAATGACTGTAGCATTCCT 59.736 43.478 0.00 0.00 33.93 3.36
1983 2499 1.789464 CGTCGCAGGCTCAATAATCTC 59.211 52.381 0.00 0.00 0.00 2.75
1995 2511 6.006449 GCTCAATAATCTCCACATACCCAAT 58.994 40.000 0.00 0.00 0.00 3.16
2014 2530 5.879223 CCCAATGGTATAGAGAAGATCATGC 59.121 44.000 0.00 0.00 0.00 4.06
2016 2532 6.594547 CCAATGGTATAGAGAAGATCATGCTG 59.405 42.308 0.00 0.00 0.00 4.41
2024 2540 8.882557 ATAGAGAAGATCATGCTGAGATAAGA 57.117 34.615 0.00 0.00 0.00 2.10
2025 2541 6.985117 AGAGAAGATCATGCTGAGATAAGAC 58.015 40.000 0.00 0.00 0.00 3.01
2047 2565 2.299521 AGACCGATGCTAGAGTGTACC 58.700 52.381 0.00 0.00 0.00 3.34
2049 2567 2.623889 GACCGATGCTAGAGTGTACCAT 59.376 50.000 0.00 0.00 0.00 3.55
2051 2569 2.288457 CCGATGCTAGAGTGTACCATGG 60.288 54.545 11.19 11.19 0.00 3.66
2053 2571 1.567357 TGCTAGAGTGTACCATGGCA 58.433 50.000 13.04 0.00 0.00 4.92
2054 2572 2.118679 TGCTAGAGTGTACCATGGCAT 58.881 47.619 13.04 0.00 0.00 4.40
2055 2573 3.304829 TGCTAGAGTGTACCATGGCATA 58.695 45.455 13.04 0.00 0.00 3.14
2056 2574 3.903714 TGCTAGAGTGTACCATGGCATAT 59.096 43.478 13.04 0.00 0.00 1.78
2057 2575 4.347876 TGCTAGAGTGTACCATGGCATATT 59.652 41.667 13.04 0.00 0.00 1.28
2058 2576 5.542251 TGCTAGAGTGTACCATGGCATATTA 59.458 40.000 13.04 0.00 0.00 0.98
2059 2577 6.213397 TGCTAGAGTGTACCATGGCATATTAT 59.787 38.462 13.04 0.00 0.00 1.28
2060 2578 6.536582 GCTAGAGTGTACCATGGCATATTATG 59.463 42.308 13.04 0.00 0.00 1.90
2079 2597 2.143122 TGCTGTCCAACTTTCATCGTC 58.857 47.619 0.00 0.00 0.00 4.20
2089 2607 0.865111 TTTCATCGTCGCACACAAGG 59.135 50.000 0.00 0.00 0.00 3.61
2112 2630 0.523072 AATGCTGTCGAACATGGCAC 59.477 50.000 0.00 0.00 33.12 5.01
2244 2762 4.606961 GACTCTACAGAGCTCTTGTATGC 58.393 47.826 15.27 6.38 45.79 3.14
2307 2825 7.037438 GGTCTATACTACAACCAACGAATTCA 58.963 38.462 6.22 0.00 0.00 2.57
2320 2838 7.881142 ACCAACGAATTCATTCACTTGAATAA 58.119 30.769 6.22 1.51 43.73 1.40
2331 2849 8.289618 TCATTCACTTGAATAACTGCTTGTAAC 58.710 33.333 4.14 0.00 42.41 2.50
2345 2863 3.185797 GCTTGTAACGAGGTGTAAAGGTG 59.814 47.826 0.00 0.00 0.00 4.00
2354 2872 2.956333 AGGTGTAAAGGTGGCTTCAAAC 59.044 45.455 0.00 0.00 0.00 2.93
2401 2919 4.371786 GGATACAAGTCATCGAAGCATCA 58.628 43.478 0.00 0.00 0.00 3.07
2438 2956 7.979444 TTTCTTTCTCCAGTGTTATAACAGG 57.021 36.000 18.56 16.42 40.05 4.00
2439 2957 5.488341 TCTTTCTCCAGTGTTATAACAGGC 58.512 41.667 18.56 8.21 40.05 4.85
2440 2958 3.906720 TCTCCAGTGTTATAACAGGCC 57.093 47.619 18.56 7.50 40.05 5.19
2441 2959 2.167693 TCTCCAGTGTTATAACAGGCCG 59.832 50.000 18.56 11.16 40.05 6.13
2442 2960 1.208535 TCCAGTGTTATAACAGGCCGG 59.791 52.381 18.56 15.16 40.05 6.13
2457 2978 1.339342 GGCCGGCTTCCTTGTTTAGTA 60.339 52.381 28.56 0.00 0.00 1.82
2521 3042 0.249955 CCCCAATCACAATGGCAACC 59.750 55.000 0.00 0.00 36.58 3.77
2569 3090 4.340666 TGAAACCAAGAAGCAGCACAATTA 59.659 37.500 0.00 0.00 0.00 1.40
2575 3096 6.032094 CCAAGAAGCAGCACAATTAACATAG 58.968 40.000 0.00 0.00 0.00 2.23
2655 3177 6.092670 CGTGATGCAAATTGGGGACTATATAG 59.907 42.308 8.27 8.27 0.00 1.31
2668 3190 9.574577 TGGGGACTATATAGAAATGTGGATAAT 57.425 33.333 16.79 0.00 0.00 1.28
2669 3191 9.838339 GGGGACTATATAGAAATGTGGATAATG 57.162 37.037 16.79 0.00 0.00 1.90
2709 3231 4.472108 ACCTCCGTTCCCAATTATAAGACA 59.528 41.667 0.00 0.00 0.00 3.41
2805 3339 8.603242 TCAGGAAAAGTTAGAACATCTTGTAC 57.397 34.615 0.00 0.00 0.00 2.90
2807 3341 8.499162 CAGGAAAAGTTAGAACATCTTGTACTG 58.501 37.037 0.00 0.00 33.02 2.74
2926 3461 8.849543 TTATCAGATTTACCTGGGTAGTAACT 57.150 34.615 0.00 0.00 34.99 2.24
2928 3463 7.893124 TCAGATTTACCTGGGTAGTAACTAG 57.107 40.000 0.00 0.00 34.99 2.57
2929 3464 7.645942 TCAGATTTACCTGGGTAGTAACTAGA 58.354 38.462 0.00 0.00 34.99 2.43
2930 3465 8.117956 TCAGATTTACCTGGGTAGTAACTAGAA 58.882 37.037 0.00 0.00 34.99 2.10
2933 3468 8.676397 ATTTACCTGGGTAGTAACTAGAAACT 57.324 34.615 0.00 1.67 29.63 2.66
2972 3511 6.980978 CACAGGGTATACTTGTGAACTATCAG 59.019 42.308 24.42 5.57 35.88 2.90
2987 3526 7.011482 GTGAACTATCAGCCTAATAACAACAGG 59.989 40.741 0.00 0.00 35.88 4.00
3055 3598 9.125026 GAGTATTTTTCATCCATGGAACATACT 57.875 33.333 20.67 18.50 45.25 2.12
3056 3599 9.125026 AGTATTTTTCATCCATGGAACATACTC 57.875 33.333 20.67 5.17 41.79 2.59
3065 3608 2.467880 TGGAACATACTCCCTCTGTCC 58.532 52.381 0.00 0.00 34.22 4.02
3066 3609 1.763545 GGAACATACTCCCTCTGTCCC 59.236 57.143 0.00 0.00 0.00 4.46
3067 3610 2.467880 GAACATACTCCCTCTGTCCCA 58.532 52.381 0.00 0.00 0.00 4.37
3068 3611 2.642171 ACATACTCCCTCTGTCCCAA 57.358 50.000 0.00 0.00 0.00 4.12
3069 3612 2.915869 ACATACTCCCTCTGTCCCAAA 58.084 47.619 0.00 0.00 0.00 3.28
3070 3613 3.256704 ACATACTCCCTCTGTCCCAAAA 58.743 45.455 0.00 0.00 0.00 2.44
3071 3614 3.852578 ACATACTCCCTCTGTCCCAAAAT 59.147 43.478 0.00 0.00 0.00 1.82
3072 3615 5.036916 ACATACTCCCTCTGTCCCAAAATA 58.963 41.667 0.00 0.00 0.00 1.40
3073 3616 5.491078 ACATACTCCCTCTGTCCCAAAATAA 59.509 40.000 0.00 0.00 0.00 1.40
3074 3617 6.160459 ACATACTCCCTCTGTCCCAAAATAAT 59.840 38.462 0.00 0.00 0.00 1.28
3075 3618 5.117406 ACTCCCTCTGTCCCAAAATAATC 57.883 43.478 0.00 0.00 0.00 1.75
3076 3619 4.790790 ACTCCCTCTGTCCCAAAATAATCT 59.209 41.667 0.00 0.00 0.00 2.40
3077 3620 5.254032 ACTCCCTCTGTCCCAAAATAATCTT 59.746 40.000 0.00 0.00 0.00 2.40
3078 3621 5.755849 TCCCTCTGTCCCAAAATAATCTTC 58.244 41.667 0.00 0.00 0.00 2.87
3079 3622 5.492524 TCCCTCTGTCCCAAAATAATCTTCT 59.507 40.000 0.00 0.00 0.00 2.85
3080 3623 6.011628 TCCCTCTGTCCCAAAATAATCTTCTT 60.012 38.462 0.00 0.00 0.00 2.52
3081 3624 7.183839 TCCCTCTGTCCCAAAATAATCTTCTTA 59.816 37.037 0.00 0.00 0.00 2.10
3082 3625 7.834181 CCCTCTGTCCCAAAATAATCTTCTTAA 59.166 37.037 0.00 0.00 0.00 1.85
3083 3626 8.678199 CCTCTGTCCCAAAATAATCTTCTTAAC 58.322 37.037 0.00 0.00 0.00 2.01
3084 3627 9.454859 CTCTGTCCCAAAATAATCTTCTTAACT 57.545 33.333 0.00 0.00 0.00 2.24
3085 3628 9.807921 TCTGTCCCAAAATAATCTTCTTAACTT 57.192 29.630 0.00 0.00 0.00 2.66
3125 3668 6.646267 ACAAAGTTGTACTAAGGTTGAGACA 58.354 36.000 0.00 0.00 40.16 3.41
3126 3669 6.537660 ACAAAGTTGTACTAAGGTTGAGACAC 59.462 38.462 0.00 0.00 40.16 3.67
3127 3670 6.481434 AAGTTGTACTAAGGTTGAGACACT 57.519 37.500 0.00 0.00 0.00 3.55
3128 3671 6.481434 AGTTGTACTAAGGTTGAGACACTT 57.519 37.500 0.00 0.00 0.00 3.16
3129 3672 7.592885 AGTTGTACTAAGGTTGAGACACTTA 57.407 36.000 0.00 0.00 0.00 2.24
3130 3673 8.191534 AGTTGTACTAAGGTTGAGACACTTAT 57.808 34.615 0.00 0.00 0.00 1.73
3131 3674 8.648693 AGTTGTACTAAGGTTGAGACACTTATT 58.351 33.333 0.00 0.00 0.00 1.40
3132 3675 9.269453 GTTGTACTAAGGTTGAGACACTTATTT 57.731 33.333 0.00 0.00 0.00 1.40
3133 3676 9.841295 TTGTACTAAGGTTGAGACACTTATTTT 57.159 29.630 0.00 0.00 0.00 1.82
3134 3677 9.268268 TGTACTAAGGTTGAGACACTTATTTTG 57.732 33.333 0.00 0.00 0.00 2.44
3135 3678 9.485206 GTACTAAGGTTGAGACACTTATTTTGA 57.515 33.333 0.00 0.00 0.00 2.69
3136 3679 8.608844 ACTAAGGTTGAGACACTTATTTTGAG 57.391 34.615 0.00 0.00 0.00 3.02
3137 3680 8.429641 ACTAAGGTTGAGACACTTATTTTGAGA 58.570 33.333 0.00 0.00 0.00 3.27
3138 3681 7.497925 AAGGTTGAGACACTTATTTTGAGAC 57.502 36.000 0.00 0.00 0.00 3.36
3139 3682 5.696724 AGGTTGAGACACTTATTTTGAGACG 59.303 40.000 0.00 0.00 0.00 4.18
3140 3683 5.107065 GGTTGAGACACTTATTTTGAGACGG 60.107 44.000 0.00 0.00 0.00 4.79
3141 3684 5.462530 TGAGACACTTATTTTGAGACGGA 57.537 39.130 0.00 0.00 0.00 4.69
3142 3685 5.470368 TGAGACACTTATTTTGAGACGGAG 58.530 41.667 0.00 0.00 0.00 4.63
3143 3686 4.822026 AGACACTTATTTTGAGACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
3144 3687 3.933332 GACACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3145 3688 3.581332 ACACTTATTTTGAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3146 3689 4.184629 CACTTATTTTGAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
3196 3741 8.378421 GCAAAACTCAAGCTAATGAAATTGATC 58.622 33.333 9.78 0.00 36.99 2.92
3236 3783 8.579682 TTCAACCAAAAACAAAACAAAAATGG 57.420 26.923 0.00 0.00 0.00 3.16
3275 3830 7.916977 CGATGGAGAAAATGCTCAAATTCATTA 59.083 33.333 0.00 0.00 36.62 1.90
3489 4044 3.245052 ACTGGAATGAGGTGAAAAGGGAG 60.245 47.826 0.00 0.00 0.00 4.30
3507 4062 3.328931 GGGAGATATGGGAAGCATCTTGA 59.671 47.826 0.00 0.00 0.00 3.02
3511 4066 6.238869 GGAGATATGGGAAGCATCTTGAAAAC 60.239 42.308 0.00 0.00 0.00 2.43
3512 4067 3.855689 ATGGGAAGCATCTTGAAAACG 57.144 42.857 0.00 0.00 0.00 3.60
3513 4068 1.269448 TGGGAAGCATCTTGAAAACGC 59.731 47.619 0.00 0.00 0.00 4.84
3514 4069 1.269448 GGGAAGCATCTTGAAAACGCA 59.731 47.619 0.00 0.00 0.00 5.24
3558 4115 9.178758 ACCAGAAGTAAAGCTAAGGAAATAATG 57.821 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 5.880901 AGGGCAAGAACTCTAAATCTTTCA 58.119 37.500 0.00 0.00 33.73 2.69
97 98 6.459573 GCACTAACAAGAAGTCAACAAATCCA 60.460 38.462 0.00 0.00 0.00 3.41
102 103 4.095782 GGTGCACTAACAAGAAGTCAACAA 59.904 41.667 17.98 0.00 0.00 2.83
128 130 0.881118 ACCATACCAGCAAAAGCACG 59.119 50.000 0.00 0.00 0.00 5.34
168 170 4.980434 TCTTCGTCGTACTTCCAAAGAAAG 59.020 41.667 0.00 0.00 0.00 2.62
174 176 3.985279 CACAATCTTCGTCGTACTTCCAA 59.015 43.478 0.00 0.00 0.00 3.53
176 178 3.829948 TCACAATCTTCGTCGTACTTCC 58.170 45.455 0.00 0.00 0.00 3.46
178 180 4.557690 CGAATCACAATCTTCGTCGTACTT 59.442 41.667 0.00 0.00 39.42 2.24
179 181 4.096311 CGAATCACAATCTTCGTCGTACT 58.904 43.478 0.00 0.00 39.42 2.73
180 182 4.093514 TCGAATCACAATCTTCGTCGTAC 58.906 43.478 4.82 0.00 43.49 3.67
185 188 4.156922 AGACTCTCGAATCACAATCTTCGT 59.843 41.667 4.82 0.00 43.49 3.85
203 206 1.196012 CCCCCTGGAAGTGTAGACTC 58.804 60.000 0.00 0.00 0.00 3.36
222 225 1.379044 CTTGGGCTGGTGATGACCC 60.379 63.158 0.00 0.00 42.34 4.46
223 226 0.962356 CACTTGGGCTGGTGATGACC 60.962 60.000 0.00 0.00 43.48 4.02
224 227 1.589716 GCACTTGGGCTGGTGATGAC 61.590 60.000 8.62 0.00 35.69 3.06
285 645 7.714377 TCAATAGAGATTTCAATGAGCTCCTTC 59.286 37.037 12.15 0.00 0.00 3.46
309 670 5.255687 ACATTGGCATGAACTTGACTATCA 58.744 37.500 0.00 0.00 34.11 2.15
311 672 5.294306 CGTACATTGGCATGAACTTGACTAT 59.706 40.000 0.00 0.00 34.11 2.12
318 679 2.009774 GCTCGTACATTGGCATGAACT 58.990 47.619 0.00 0.00 34.11 3.01
327 688 2.798501 CGCCACCGCTCGTACATTG 61.799 63.158 0.00 0.00 0.00 2.82
363 724 6.183360 CCAAGGGTTCAACTAAGATAATGCAG 60.183 42.308 0.00 0.00 0.00 4.41
368 729 5.249780 TGCCAAGGGTTCAACTAAGATAA 57.750 39.130 0.00 0.00 0.00 1.75
382 743 5.307204 TGAAAGATGAAATTTTGCCAAGGG 58.693 37.500 0.00 0.00 0.00 3.95
419 780 2.961526 TTCAGATACGCCTTCTCCAC 57.038 50.000 0.00 0.00 0.00 4.02
420 781 3.096852 TCTTTCAGATACGCCTTCTCCA 58.903 45.455 0.00 0.00 0.00 3.86
428 789 5.572211 TGCAATCAAATCTTTCAGATACGC 58.428 37.500 0.00 0.00 32.89 4.42
445 806 7.854534 AGCTGTTGAAACTAAAAATTGCAATC 58.145 30.769 13.38 0.00 0.00 2.67
495 933 5.776744 ACGTACTACGAATGGAAAAGTCTT 58.223 37.500 15.49 0.00 46.05 3.01
497 935 7.746526 AATACGTACTACGAATGGAAAAGTC 57.253 36.000 15.49 0.00 46.05 3.01
498 936 8.462016 AGTAATACGTACTACGAATGGAAAAGT 58.538 33.333 15.49 0.00 46.05 2.66
501 939 7.910162 GTGAGTAATACGTACTACGAATGGAAA 59.090 37.037 15.49 0.00 46.05 3.13
508 946 4.740205 CGGAGTGAGTAATACGTACTACGA 59.260 45.833 21.53 0.00 46.05 3.43
509 947 4.504461 ACGGAGTGAGTAATACGTACTACG 59.496 45.833 23.17 23.17 43.45 3.51
513 951 5.631026 TGAAACGGAGTGAGTAATACGTAC 58.369 41.667 0.00 0.00 45.00 3.67
517 955 9.362539 TCTATTTTGAAACGGAGTGAGTAATAC 57.637 33.333 0.00 0.00 45.00 1.89
519 957 8.883731 CATCTATTTTGAAACGGAGTGAGTAAT 58.116 33.333 0.00 0.00 45.00 1.89
521 959 7.544566 GTCATCTATTTTGAAACGGAGTGAGTA 59.455 37.037 0.00 0.00 45.00 2.59
522 960 6.369065 GTCATCTATTTTGAAACGGAGTGAGT 59.631 38.462 0.00 0.00 45.00 3.41
523 961 6.591834 AGTCATCTATTTTGAAACGGAGTGAG 59.408 38.462 0.00 0.00 45.00 3.51
525 963 6.454318 CGAGTCATCTATTTTGAAACGGAGTG 60.454 42.308 0.00 0.00 45.00 3.51
528 966 5.575606 GTCGAGTCATCTATTTTGAAACGGA 59.424 40.000 0.00 0.00 0.00 4.69
529 967 5.577164 AGTCGAGTCATCTATTTTGAAACGG 59.423 40.000 0.00 0.00 0.00 4.44
530 968 6.633668 AGTCGAGTCATCTATTTTGAAACG 57.366 37.500 0.00 0.00 0.00 3.60
582 1020 8.673711 CGATTCAAAATAGATGACCCAACTTTA 58.326 33.333 0.00 0.00 0.00 1.85
583 1021 7.362920 CCGATTCAAAATAGATGACCCAACTTT 60.363 37.037 0.00 0.00 0.00 2.66
584 1022 6.095440 CCGATTCAAAATAGATGACCCAACTT 59.905 38.462 0.00 0.00 0.00 2.66
585 1023 5.590259 CCGATTCAAAATAGATGACCCAACT 59.410 40.000 0.00 0.00 0.00 3.16
586 1024 5.588648 TCCGATTCAAAATAGATGACCCAAC 59.411 40.000 0.00 0.00 0.00 3.77
587 1025 5.750524 TCCGATTCAAAATAGATGACCCAA 58.249 37.500 0.00 0.00 0.00 4.12
588 1026 5.366482 TCCGATTCAAAATAGATGACCCA 57.634 39.130 0.00 0.00 0.00 4.51
589 1027 5.182001 CCATCCGATTCAAAATAGATGACCC 59.818 44.000 11.14 0.00 34.40 4.46
590 1028 5.997746 TCCATCCGATTCAAAATAGATGACC 59.002 40.000 11.14 0.00 34.40 4.02
591 1029 6.708054 ACTCCATCCGATTCAAAATAGATGAC 59.292 38.462 11.14 0.00 34.40 3.06
592 1030 6.830912 ACTCCATCCGATTCAAAATAGATGA 58.169 36.000 11.14 0.00 34.40 2.92
593 1031 7.875041 AGTACTCCATCCGATTCAAAATAGATG 59.125 37.037 0.00 0.00 0.00 2.90
594 1032 7.967908 AGTACTCCATCCGATTCAAAATAGAT 58.032 34.615 0.00 0.00 0.00 1.98
595 1033 7.361457 AGTACTCCATCCGATTCAAAATAGA 57.639 36.000 0.00 0.00 0.00 1.98
596 1034 8.361139 ACTAGTACTCCATCCGATTCAAAATAG 58.639 37.037 0.00 0.00 0.00 1.73
597 1035 8.246430 ACTAGTACTCCATCCGATTCAAAATA 57.754 34.615 0.00 0.00 0.00 1.40
598 1036 7.125792 ACTAGTACTCCATCCGATTCAAAAT 57.874 36.000 0.00 0.00 0.00 1.82
599 1037 6.540438 ACTAGTACTCCATCCGATTCAAAA 57.460 37.500 0.00 0.00 0.00 2.44
600 1038 6.540438 AACTAGTACTCCATCCGATTCAAA 57.460 37.500 0.00 0.00 0.00 2.69
601 1039 6.238953 GCTAACTAGTACTCCATCCGATTCAA 60.239 42.308 0.00 0.00 0.00 2.69
602 1040 5.241064 GCTAACTAGTACTCCATCCGATTCA 59.759 44.000 0.00 0.00 0.00 2.57
603 1041 5.474189 AGCTAACTAGTACTCCATCCGATTC 59.526 44.000 0.00 0.00 0.00 2.52
604 1042 5.241949 CAGCTAACTAGTACTCCATCCGATT 59.758 44.000 0.00 0.00 0.00 3.34
605 1043 4.762765 CAGCTAACTAGTACTCCATCCGAT 59.237 45.833 0.00 0.00 0.00 4.18
606 1044 4.135306 CAGCTAACTAGTACTCCATCCGA 58.865 47.826 0.00 0.00 0.00 4.55
607 1045 3.304794 GCAGCTAACTAGTACTCCATCCG 60.305 52.174 0.00 0.00 0.00 4.18
608 1046 3.006003 GGCAGCTAACTAGTACTCCATCC 59.994 52.174 0.00 0.00 0.00 3.51
609 1047 3.006003 GGGCAGCTAACTAGTACTCCATC 59.994 52.174 0.00 0.00 0.00 3.51
610 1048 2.966516 GGGCAGCTAACTAGTACTCCAT 59.033 50.000 0.00 0.00 0.00 3.41
611 1049 2.291996 TGGGCAGCTAACTAGTACTCCA 60.292 50.000 0.00 0.00 0.00 3.86
612 1050 2.385803 TGGGCAGCTAACTAGTACTCC 58.614 52.381 0.00 0.00 0.00 3.85
613 1051 4.342665 AGATTGGGCAGCTAACTAGTACTC 59.657 45.833 0.00 0.00 0.00 2.59
614 1052 4.290942 AGATTGGGCAGCTAACTAGTACT 58.709 43.478 0.00 0.00 0.00 2.73
619 1057 2.362397 CTCGAGATTGGGCAGCTAACTA 59.638 50.000 6.58 0.00 0.00 2.24
637 1075 1.148310 ACAAACAATGGCGAGACTCG 58.852 50.000 20.56 20.56 43.89 4.18
655 1093 2.148768 CTTCCACCGTACCTTCCAAAC 58.851 52.381 0.00 0.00 0.00 2.93
656 1094 2.048601 TCTTCCACCGTACCTTCCAAA 58.951 47.619 0.00 0.00 0.00 3.28
657 1095 1.719529 TCTTCCACCGTACCTTCCAA 58.280 50.000 0.00 0.00 0.00 3.53
658 1096 1.719529 TTCTTCCACCGTACCTTCCA 58.280 50.000 0.00 0.00 0.00 3.53
677 1115 4.102838 TGCCTGCAATTATTGGGCATTATT 59.897 37.500 19.13 0.00 41.18 1.40
680 1118 1.838715 TGCCTGCAATTATTGGGCATT 59.161 42.857 19.13 0.00 41.18 3.56
683 1121 1.066286 TGTTGCCTGCAATTATTGGGC 60.066 47.619 15.24 15.24 38.28 5.36
696 1134 1.004044 CATGTCCTCTTCCTGTTGCCT 59.996 52.381 0.00 0.00 0.00 4.75
715 1153 1.136891 ACGGTGAAGCATCGATCATCA 59.863 47.619 7.12 0.00 40.81 3.07
722 1160 3.554692 GCGGACGGTGAAGCATCG 61.555 66.667 0.00 0.00 44.22 3.84
759 1197 1.064017 TCCCCATGGAATTGGCAGTAC 60.064 52.381 15.22 0.00 37.86 2.73
762 1200 0.032813 ACTCCCCATGGAATTGGCAG 60.033 55.000 15.22 7.81 41.17 4.85
763 1201 0.413037 AACTCCCCATGGAATTGGCA 59.587 50.000 15.22 0.00 41.17 4.92
764 1202 1.207811 CAAACTCCCCATGGAATTGGC 59.792 52.381 15.22 0.00 41.17 4.52
776 1214 0.536460 TCCGTTTCCTGCAAACTCCC 60.536 55.000 0.00 0.00 42.17 4.30
803 1241 1.663702 CCGTCCCCATTATCGACGC 60.664 63.158 3.42 0.00 46.09 5.19
892 1341 2.684104 GGAAGGGAAGGGAAGGGC 59.316 66.667 0.00 0.00 0.00 5.19
1345 1804 2.544069 CGAGGGCTTAATCGAGGAAGAC 60.544 54.545 12.11 9.35 41.40 3.01
1348 1807 1.407979 GACGAGGGCTTAATCGAGGAA 59.592 52.381 3.36 0.00 41.40 3.36
1432 1901 2.766400 CGACTCCCTCTCTGCGGAC 61.766 68.421 0.00 0.00 0.00 4.79
1433 1902 2.438614 CGACTCCCTCTCTGCGGA 60.439 66.667 0.00 0.00 0.00 5.54
1435 1904 4.544689 CGCGACTCCCTCTCTGCG 62.545 72.222 0.00 0.00 39.57 5.18
1436 1905 4.200283 CCGCGACTCCCTCTCTGC 62.200 72.222 8.23 0.00 0.00 4.26
1437 1906 4.200283 GCCGCGACTCCCTCTCTG 62.200 72.222 8.23 0.00 0.00 3.35
1438 1907 4.742649 TGCCGCGACTCCCTCTCT 62.743 66.667 8.23 0.00 0.00 3.10
1439 1908 4.200283 CTGCCGCGACTCCCTCTC 62.200 72.222 8.23 0.00 0.00 3.20
1455 1924 0.326264 GCAGGACTTCACATCACCCT 59.674 55.000 0.00 0.00 0.00 4.34
1467 1936 0.251386 TCGGTCTTCAGAGCAGGACT 60.251 55.000 6.81 0.00 42.28 3.85
1477 1946 3.193757 CGATCCGGTCGGTCTTCA 58.806 61.111 15.79 0.00 46.47 3.02
1550 2020 1.773054 CTAGCTAGCTTCCGACGCGA 61.773 60.000 24.88 0.00 0.00 5.87
1551 2021 1.369448 CTAGCTAGCTTCCGACGCG 60.369 63.158 24.88 3.53 0.00 6.01
1552 2022 0.942962 TACTAGCTAGCTTCCGACGC 59.057 55.000 24.88 0.00 0.00 5.19
1553 2023 1.069771 GCTACTAGCTAGCTTCCGACG 60.070 57.143 24.88 8.18 44.24 5.12
1554 2024 1.267533 GGCTACTAGCTAGCTTCCGAC 59.732 57.143 24.88 10.22 46.53 4.79
1555 2025 1.143277 AGGCTACTAGCTAGCTTCCGA 59.857 52.381 24.88 3.23 46.53 4.55
1556 2026 1.611519 AGGCTACTAGCTAGCTTCCG 58.388 55.000 24.88 14.11 46.53 4.30
1576 2057 1.561643 TGTTGCAGAGGCTAGCTACT 58.438 50.000 15.72 11.23 41.91 2.57
1621 2106 5.776744 ACAAGCCTTTTTCTGATTGATGTC 58.223 37.500 0.00 0.00 0.00 3.06
1689 2181 3.618780 GAGTCCCTGCCAGGTGCTG 62.619 68.421 10.47 0.00 42.00 4.41
1725 2217 7.603651 CCGAAGGCATGATTATTACTACTAGT 58.396 38.462 0.00 0.00 46.14 2.57
1749 2241 0.374758 CATGTATGCGTGCAGTCACC 59.625 55.000 2.42 0.00 40.04 4.02
1773 2265 2.670414 CACGACAGGAGCTGAAGATTTC 59.330 50.000 0.00 0.00 35.18 2.17
1794 2286 5.107989 CGTGACGGTAGCATATATGTTTGAC 60.108 44.000 14.14 4.51 0.00 3.18
1839 2337 1.580845 CTCCTTTCAGCGCACCCAAG 61.581 60.000 11.47 5.91 0.00 3.61
1844 2342 2.684843 CCAGCTCCTTTCAGCGCAC 61.685 63.158 11.47 0.00 44.82 5.34
1845 2343 2.359107 CCAGCTCCTTTCAGCGCA 60.359 61.111 11.47 0.00 44.82 6.09
1846 2344 3.808656 GCCAGCTCCTTTCAGCGC 61.809 66.667 0.00 0.00 44.82 5.92
1873 2371 4.346129 GCAACTCATCTAAAAGGAATGCG 58.654 43.478 0.00 0.00 0.00 4.73
1879 2377 1.401905 GCGGGCAACTCATCTAAAAGG 59.598 52.381 0.00 0.00 0.00 3.11
1888 2386 3.430862 GCAATCGCGGGCAACTCA 61.431 61.111 6.13 0.00 0.00 3.41
1897 2395 2.549633 ATTCTTTCCTTGCAATCGCG 57.450 45.000 0.00 0.00 42.97 5.87
1929 2434 2.099141 TGCTACAGTCATTGGTGAGC 57.901 50.000 0.00 0.00 34.36 4.26
2014 2530 4.047822 GCATCGGTCTTGTCTTATCTCAG 58.952 47.826 0.00 0.00 0.00 3.35
2016 2532 4.314740 AGCATCGGTCTTGTCTTATCTC 57.685 45.455 0.00 0.00 0.00 2.75
2024 2540 2.171840 ACACTCTAGCATCGGTCTTGT 58.828 47.619 0.00 0.00 0.00 3.16
2025 2541 2.949451 ACACTCTAGCATCGGTCTTG 57.051 50.000 0.00 0.00 0.00 3.02
2053 2571 6.767902 ACGATGAAAGTTGGACAGCATAATAT 59.232 34.615 0.00 0.00 0.00 1.28
2054 2572 6.112734 ACGATGAAAGTTGGACAGCATAATA 58.887 36.000 0.00 0.00 0.00 0.98
2055 2573 4.943705 ACGATGAAAGTTGGACAGCATAAT 59.056 37.500 0.00 0.00 0.00 1.28
2056 2574 4.323417 ACGATGAAAGTTGGACAGCATAA 58.677 39.130 0.00 0.00 0.00 1.90
2057 2575 3.932710 GACGATGAAAGTTGGACAGCATA 59.067 43.478 0.00 0.00 0.00 3.14
2058 2576 2.744202 GACGATGAAAGTTGGACAGCAT 59.256 45.455 0.00 0.00 0.00 3.79
2059 2577 2.143122 GACGATGAAAGTTGGACAGCA 58.857 47.619 0.00 0.00 0.00 4.41
2060 2578 1.126846 CGACGATGAAAGTTGGACAGC 59.873 52.381 0.00 0.00 0.00 4.40
2061 2579 1.126846 GCGACGATGAAAGTTGGACAG 59.873 52.381 0.00 0.00 0.00 3.51
2062 2580 1.144969 GCGACGATGAAAGTTGGACA 58.855 50.000 0.00 0.00 0.00 4.02
2063 2581 1.136336 GTGCGACGATGAAAGTTGGAC 60.136 52.381 0.00 0.00 37.22 4.02
2064 2582 1.144969 GTGCGACGATGAAAGTTGGA 58.855 50.000 0.00 0.00 0.00 3.53
2065 2583 0.865111 TGTGCGACGATGAAAGTTGG 59.135 50.000 0.00 0.00 0.00 3.77
2066 2584 1.260297 TGTGTGCGACGATGAAAGTTG 59.740 47.619 0.00 0.00 0.00 3.16
2067 2585 1.577468 TGTGTGCGACGATGAAAGTT 58.423 45.000 0.00 0.00 0.00 2.66
2079 2597 0.877071 AGCATTCTTCCTTGTGTGCG 59.123 50.000 0.00 0.00 37.63 5.34
2089 2607 2.476854 GCCATGTTCGACAGCATTCTTC 60.477 50.000 0.00 0.00 0.00 2.87
2112 2630 0.664761 CCGCCCTTGACTGCATAATG 59.335 55.000 0.00 0.00 0.00 1.90
2307 2825 7.172532 TCGTTACAAGCAGTTATTCAAGTGAAT 59.827 33.333 11.13 11.13 45.77 2.57
2320 2838 3.738830 TTACACCTCGTTACAAGCAGT 57.261 42.857 0.00 0.00 0.00 4.40
2331 2849 1.270625 TGAAGCCACCTTTACACCTCG 60.271 52.381 0.00 0.00 0.00 4.63
2345 2863 2.413837 TCAAGCGAGTAGTTTGAAGCC 58.586 47.619 0.13 0.00 45.07 4.35
2354 2872 1.078759 CTGCCCGTTCAAGCGAGTAG 61.079 60.000 0.00 0.00 0.00 2.57
2437 2955 0.608308 ACTAAACAAGGAAGCCGGCC 60.608 55.000 26.15 8.83 0.00 6.13
2438 2956 2.007608 CTACTAAACAAGGAAGCCGGC 58.992 52.381 21.89 21.89 0.00 6.13
2439 2957 3.604875 TCTACTAAACAAGGAAGCCGG 57.395 47.619 0.00 0.00 0.00 6.13
2440 2958 5.063564 GTGATTCTACTAAACAAGGAAGCCG 59.936 44.000 0.00 0.00 0.00 5.52
2441 2959 5.354513 GGTGATTCTACTAAACAAGGAAGCC 59.645 44.000 0.00 0.00 0.00 4.35
2442 2960 5.938125 TGGTGATTCTACTAAACAAGGAAGC 59.062 40.000 0.00 0.00 0.00 3.86
2457 2978 5.591877 GCCAAGAACAAGATATGGTGATTCT 59.408 40.000 0.00 0.00 33.63 2.40
2521 3042 2.797156 CTTCATTCGGAAGTATGCTCCG 59.203 50.000 12.95 12.95 46.49 4.63
2606 3127 6.462949 CGATCTGCGTATTTCTGAAAAAGTTC 59.537 38.462 6.95 4.72 34.64 3.01
2668 3190 6.097839 ACGGAGGTGATACTTTATTAGCTTCA 59.902 38.462 0.00 0.00 33.41 3.02
2669 3191 6.514063 ACGGAGGTGATACTTTATTAGCTTC 58.486 40.000 0.00 0.00 33.41 3.86
2740 3264 5.583061 ACGTGTTTGTTCACTCATTTCAGTA 59.417 36.000 0.00 0.00 36.33 2.74
2805 3339 3.187700 CTCCCTCCGTTTCGAATTACAG 58.812 50.000 0.00 0.00 0.00 2.74
2807 3341 3.242549 ACTCCCTCCGTTTCGAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
2916 3451 7.148289 GCAAAATGGAGTTTCTAGTTACTACCC 60.148 40.741 6.73 3.57 0.00 3.69
2925 3460 6.206634 TGTGGTTAGCAAAATGGAGTTTCTAG 59.793 38.462 0.00 0.00 0.00 2.43
2926 3461 6.065374 TGTGGTTAGCAAAATGGAGTTTCTA 58.935 36.000 0.00 0.00 0.00 2.10
2928 3463 5.195001 TGTGGTTAGCAAAATGGAGTTTC 57.805 39.130 0.00 0.00 0.00 2.78
2929 3464 4.039124 CCTGTGGTTAGCAAAATGGAGTTT 59.961 41.667 0.00 0.00 0.00 2.66
2930 3465 3.573967 CCTGTGGTTAGCAAAATGGAGTT 59.426 43.478 0.00 0.00 0.00 3.01
2933 3468 2.158385 ACCCTGTGGTTAGCAAAATGGA 60.158 45.455 0.00 0.00 44.75 3.41
2959 3498 7.880713 TGTTGTTATTAGGCTGATAGTTCACAA 59.119 33.333 9.10 9.10 0.00 3.33
2987 3526 8.512138 ACTAAAGTTTATATGCTTCCAACACAC 58.488 33.333 0.00 0.00 0.00 3.82
3052 3595 5.970640 AGATTATTTTGGGACAGAGGGAGTA 59.029 40.000 0.00 0.00 42.39 2.59
3053 3596 4.790790 AGATTATTTTGGGACAGAGGGAGT 59.209 41.667 0.00 0.00 42.39 3.85
3054 3597 5.379706 AGATTATTTTGGGACAGAGGGAG 57.620 43.478 0.00 0.00 42.39 4.30
3055 3598 5.492524 AGAAGATTATTTTGGGACAGAGGGA 59.507 40.000 0.00 0.00 42.39 4.20
3056 3599 5.760131 AGAAGATTATTTTGGGACAGAGGG 58.240 41.667 0.00 0.00 42.39 4.30
3057 3600 8.678199 GTTAAGAAGATTATTTTGGGACAGAGG 58.322 37.037 0.00 0.00 42.39 3.69
3058 3601 9.454859 AGTTAAGAAGATTATTTTGGGACAGAG 57.545 33.333 0.00 0.00 42.39 3.35
3059 3602 9.807921 AAGTTAAGAAGATTATTTTGGGACAGA 57.192 29.630 0.00 0.00 42.39 3.41
3100 3643 7.707893 GTGTCTCAACCTTAGTACAACTTTGTA 59.292 37.037 0.00 0.00 42.35 2.41
3101 3644 6.537660 GTGTCTCAACCTTAGTACAACTTTGT 59.462 38.462 0.00 0.00 44.86 2.83
3102 3645 6.761714 AGTGTCTCAACCTTAGTACAACTTTG 59.238 38.462 0.00 0.00 0.00 2.77
3103 3646 6.885922 AGTGTCTCAACCTTAGTACAACTTT 58.114 36.000 0.00 0.00 0.00 2.66
3104 3647 6.481434 AGTGTCTCAACCTTAGTACAACTT 57.519 37.500 0.00 0.00 0.00 2.66
3105 3648 6.481434 AAGTGTCTCAACCTTAGTACAACT 57.519 37.500 0.00 0.00 0.00 3.16
3106 3649 8.828688 AATAAGTGTCTCAACCTTAGTACAAC 57.171 34.615 0.00 0.00 0.00 3.32
3107 3650 9.841295 AAAATAAGTGTCTCAACCTTAGTACAA 57.159 29.630 0.00 0.00 0.00 2.41
3108 3651 9.268268 CAAAATAAGTGTCTCAACCTTAGTACA 57.732 33.333 0.00 0.00 0.00 2.90
3109 3652 9.485206 TCAAAATAAGTGTCTCAACCTTAGTAC 57.515 33.333 0.00 0.00 0.00 2.73
3110 3653 9.706691 CTCAAAATAAGTGTCTCAACCTTAGTA 57.293 33.333 0.00 0.00 0.00 1.82
3111 3654 8.429641 TCTCAAAATAAGTGTCTCAACCTTAGT 58.570 33.333 0.00 0.00 0.00 2.24
3112 3655 8.713271 GTCTCAAAATAAGTGTCTCAACCTTAG 58.287 37.037 0.00 0.00 0.00 2.18
3113 3656 7.384115 CGTCTCAAAATAAGTGTCTCAACCTTA 59.616 37.037 0.00 0.00 0.00 2.69
3114 3657 6.202954 CGTCTCAAAATAAGTGTCTCAACCTT 59.797 38.462 0.00 0.00 0.00 3.50
3115 3658 5.696724 CGTCTCAAAATAAGTGTCTCAACCT 59.303 40.000 0.00 0.00 0.00 3.50
3116 3659 5.107065 CCGTCTCAAAATAAGTGTCTCAACC 60.107 44.000 0.00 0.00 0.00 3.77
3117 3660 5.694910 TCCGTCTCAAAATAAGTGTCTCAAC 59.305 40.000 0.00 0.00 0.00 3.18
3118 3661 5.849510 TCCGTCTCAAAATAAGTGTCTCAA 58.150 37.500 0.00 0.00 0.00 3.02
3119 3662 5.462530 TCCGTCTCAAAATAAGTGTCTCA 57.537 39.130 0.00 0.00 0.00 3.27
3120 3663 4.865365 CCTCCGTCTCAAAATAAGTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
3121 3664 4.322801 CCCTCCGTCTCAAAATAAGTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
3122 3665 3.933332 CCCTCCGTCTCAAAATAAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
3123 3666 3.581332 TCCCTCCGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
3124 3667 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
3125 3668 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
3126 3669 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
3127 3670 4.773674 TGTACTCCCTCCGTCTCAAAATAA 59.226 41.667 0.00 0.00 0.00 1.40
3128 3671 4.346730 TGTACTCCCTCCGTCTCAAAATA 58.653 43.478 0.00 0.00 0.00 1.40
3129 3672 3.170717 TGTACTCCCTCCGTCTCAAAAT 58.829 45.455 0.00 0.00 0.00 1.82
3130 3673 2.600790 TGTACTCCCTCCGTCTCAAAA 58.399 47.619 0.00 0.00 0.00 2.44
3131 3674 2.297698 TGTACTCCCTCCGTCTCAAA 57.702 50.000 0.00 0.00 0.00 2.69
3132 3675 2.526888 ATGTACTCCCTCCGTCTCAA 57.473 50.000 0.00 0.00 0.00 3.02
3133 3676 2.526888 AATGTACTCCCTCCGTCTCA 57.473 50.000 0.00 0.00 0.00 3.27
3134 3677 3.025262 AGAAATGTACTCCCTCCGTCTC 58.975 50.000 0.00 0.00 0.00 3.36
3135 3678 3.103080 AGAAATGTACTCCCTCCGTCT 57.897 47.619 0.00 0.00 0.00 4.18
3136 3679 3.889520 AAGAAATGTACTCCCTCCGTC 57.110 47.619 0.00 0.00 0.00 4.79
3137 3680 3.581332 TCAAAGAAATGTACTCCCTCCGT 59.419 43.478 0.00 0.00 0.00 4.69
3138 3681 4.202245 TCAAAGAAATGTACTCCCTCCG 57.798 45.455 0.00 0.00 0.00 4.63
3139 3682 4.336713 GCATCAAAGAAATGTACTCCCTCC 59.663 45.833 0.00 0.00 0.00 4.30
3140 3683 5.189180 AGCATCAAAGAAATGTACTCCCTC 58.811 41.667 0.00 0.00 0.00 4.30
3141 3684 5.184892 AGCATCAAAGAAATGTACTCCCT 57.815 39.130 0.00 0.00 0.00 4.20
3142 3685 5.415701 TGAAGCATCAAAGAAATGTACTCCC 59.584 40.000 0.00 0.00 30.99 4.30
3143 3686 6.500684 TGAAGCATCAAAGAAATGTACTCC 57.499 37.500 0.00 0.00 30.99 3.85
3144 3687 7.025963 CCTTGAAGCATCAAAGAAATGTACTC 58.974 38.462 5.79 0.00 44.64 2.59
3145 3688 6.071728 CCCTTGAAGCATCAAAGAAATGTACT 60.072 38.462 5.79 0.00 44.64 2.73
3146 3689 6.095377 CCCTTGAAGCATCAAAGAAATGTAC 58.905 40.000 5.79 0.00 44.64 2.90
3228 3774 6.978343 TCGTAGTCAGGAATACCATTTTTG 57.022 37.500 1.77 0.00 38.94 2.44
3236 3783 5.769484 TTCTCCATCGTAGTCAGGAATAC 57.231 43.478 0.00 0.00 0.00 1.89
3489 4044 5.514279 CGTTTTCAAGATGCTTCCCATATC 58.486 41.667 0.00 0.00 33.29 1.63
3526 4081 2.930950 AGCTTTACTTCTGGTGCACAA 58.069 42.857 20.43 6.43 0.00 3.33
3527 4082 2.638480 AGCTTTACTTCTGGTGCACA 57.362 45.000 20.43 3.92 0.00 4.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.